Until well in the 17th century the Mennonite congregations in Holland were served by lay preachers. In the 17th century an attempt was made to meet the rising educational level and the interest in art and science by choosing the best-educated men possible, usually physicians. But many congregations were not thriving, and many were near extinction. At a meeting of the Waterlander Societeit at Haarlem in 1675, Jan van Ranst expressed his grave concern about this serious condition, the church board of the Rotterdam congregation having already written about it to Galenus Abrahamsz de Haan in Amsterdam. The congregations of Rotterdam and Leiden were ready to establish a seminary, but Haarlem opposed it, considering scholarly learning superfluous for a preacher. Then the deacons of the Amsterdam Lamist and Toren congregation passed a resolution in 1680 which gave de Haan charge of training several young people for the ministry. With modest means and a small library he did the best he could to fulfill his obligation. After his death the students had to continue their studies at the Remonstrant seminary, where they had heard lectures before. A far-reaching fraternization resulted, so that finally the Mennonite congregations chose Remonstrant candidates to fill their pulpits, a policy the Remonstrants were compelled to oppose in their own interest.

Then the council of the Amsterdam Lamist and Toren congregation decided to urge the establishment of a seminary of its own. An attempt was made for a union or association of congregations which would be responsible for the new seminary, but there was little interest. Only six congregations were represented at the meeting; the Zonist congregation wanted to bind the professor to a creed, and other congregations had financial doubts. Thereupon the Lamist and Toren congregation of Amsterdam opened the Mennonite seminary at its own expense, furnishing the salary of the professor and scholarships for six to eight students. Tjerk Nieuwenhuis was appointed professor (1735-1759). In 1753 the Zonist congregation of Amsterdam appointed Petrus Smidt, one of its preachers, as a professor to train preachers for its own group, but after his death (1781) no successor could be found. From this time on the preachers for the Zonist congregations were educated either by competent preachers of the group or at the Lamist seminary. This was the status until 1801.

At the Lamist seminary Professor Nieuwenhuis was succeeded by Heere Oosterbaan from 1761 to 1785, and Gerrit Hesselink from 1786 to 1811. The Amsterdam church had generously opened its seminary to outside Mennonite students, who were supported by other congregations or supported themselves. Students of other denominations were also admitted, and Mennonite students attended lectures in philosophy and church history at the Remonstrant seminary and at the Amsterdam Athenaeum. A board of curators had the supervision; a regulation of 1737 controlled instruction and contained among others the 18 doctrinal questions on which the students were examined before they were appointed to the ministry. The first two professors were philosophers rather than theologians; in keeping with the current philosophical trend in Holland they taught natural science, especially physics and mathematics (applied philosophy). The church council provided the equipment for a laboratory for their teaching. In 1780 the seminary enjoyed its most flourishing period with 18 students.

Under Hesselink, who distinguished himself as a theologian by his exegetical dictionary of the New Testament, the crisis came. Financially weakened by the French occupation, the Amsterdam combined Lamist and Zonist congregation could no longer support the seminary alone, and appealed to other congregations for aid. In 1811 the Algemene Doopsgezinde Sociëteit (ADS) was organized, with its main purpose to assume the support and management of the Mennonite seminary, and to assist the poorer congregations by the improvement of salaries for preachers. Without compulsion of any kind it succeeded in bringing all the Dutch congregations into the ADS and in making the transition to a salaried, trained ministry. Hesselink lived to witness the founding of the ADS. His successor was Rinse Koopmans, a thorough scholar, who wore himself out in service for his fellow church members. After his death a change was made in the plan of instruction. In 1827 Samuel Muller was chosen professor of dogmatics, practical theology and—an innovation—Mennonite history; and in the same year Wopko Cnoop Koopmans, the son of Rinse Koopmans, was chosen professor of exegesis, general church history and ethics. An interest in the past awoke, as is shown by the writings of Steven Blaupot ten Cate, Alle Meenderts Cramer and Samuel Muller. Since then there have always been two professors at the seminary. Jan van Gilse (1849-1859),Sytse Hoekstra (1847-1892), and Jacob G. de Hoop Scheffer (1860-1890) were the occupants of the professorships during the heart of the 19th century.

All of these men are honored in the world of scholarship, but they also were potent forces in the advancement of new spiritual life. Under Hoekstra and de Hoop Scheffer modern theology began its growth in Holland; they were the first professors to teach at the same time at the University of Amsterdam. Until 1871 the seminary professors gave only a part of the general theological instruction; for their study in languages and philosophy the students had to attend the Athenaeum. In 1876 a law was passed requiring a theological department at the University of Amsterdam, the former Athenaeum. Hoekstra was appointed for systematic theology and de Hoop Scheffer for Semitic languages. Arrangements for instruction were altered to the extent of requiring Mennonite theological students to take university examinations and limiting seminary instruction to dogmatics, ethics, practical theology with practice in preaching and lecturing, cursory reading of the New Testament and Mennonite history and principles.

In 1907 women were first admitted as students at the seminary. In 1950, 34 students were enrolled at the seminary (12 of them women). By the 1950s the board of directors of the seminary consisted of seven members of the directorate of the Algemene Doopsgezinde Sociëteit and the professors. The number of students at the seminary, which during the first half of the 19th century scarcely exceeded 20, reached its peak in 1895 with 51 students, and decreased thereafter (33 in 1900, 16 in 1906, 33 in 1939 and 24 in 1952).

A great aid to study was offered by the [[Amsterdam Mennonite Library (Bibliotheek en Archief van de Vereenigde
Doopsgezinde Gemeente te Amsterdam)|library of the Amsterdam Mennonite church]]. The significance of the Mennonite seminary lay in the fact that it trained future ministers for the performance of their office in accordance with the needs of the brotherhood, that it acquainted the students with the Mennonite past, thus strengthening the love for the brotherhood, that it gave them instruction in doctrine, which was under the influence of tradition, and that it—a gain that must not be undervalued—promoted fellowship among the Mennonite students. These were all things that a university cannot offer.

By the 1950s there were only very few Dutch congregations that did not have a theologically trained minister. Nearly all ministers attended the University of Amsterdam and the Mennonite Theological Seminary. The cooperation between these two institutions continued to be harmonious. The entrance requirements for each was graduation from a humanistic "gymnasium." The combined theological training at the university and seminary required at least five years. After having passed the examinations at either institution the student became a proponent—a ministerial candidate—of the ADS. Under the sponsorship of the latter he now preached his trial sermons in various congregations where there were vacancies until he was placed.

In no other country have the Mennonites had a theological seminary of such long standing nor have the ministers received such uniform and thorough theological training as is the case in Holland. A few Mennonites of other countries have attended the Mennonite Seminary of Amsterdam and after World War II some of the Dutch theological students studied in American Mennonite colleges as exchange students.

In 2003 the Amsterdam Mennonite Seminary became affiliated with the Free University of Amsterdam (Vrije Universiteit Amsterdam) where a large Reformed-background theology was in place.